Visualizations for Microbiome Community Description and Anomaly Detection in Dairy Samples

## Histophilus}, \textit{Rahnella}, \textit{Raoultella}, \textit{T4virus}, \textit{Pragia}, \textit{C2virus}, \textit{Methylophilus}, \textit{Oceanobacillus}, \textit{Streptosporangium}, \textit{Fluviicola}, \textit{Oenococcus}, \textit{Alkalilimnicola}, \textit{Geminocystis}, \textit{Brevibacillus
##  [1] "Baseline_01_2018.09.05"     "Baseline_02_2018.09.06"    
##  [3] "Baseline_03_2018.09.07"     "Baseline_04_2018.09.08"    
##  [5] "Baseline_05_2018.09.09"     "Baseline_06_2018.09.10"    
##  [7] "Baseline_07_2018.09.11"     "Baseline_08_2018.09.12"    
##  [9] "Baseline_09_2018.09.13"     "Baseline_10_2018.09.14"    
## [11] "Baseline_11_2018.09.15"     "Baseline_12_2018.09.16"    
## [13] "Baseline_13_2018.09.17"     "Baseline_14_2018.09.18"    
## [15] "Baseline_15_2018.09.19"     "Baseline_16_2018.09.20"    
## [17] "Baseline_17_2018.09.21"     "Baseline_18_2018.09.22"    
## [19] "Baseline_19_2018.09.23"     "Baseline_20_2018.09.24"    
## [21] "Baseline_21_2018.09.25"     "Baseline_22_2018.09.26"    
## [23] "Baseline_23_2018.09.27"     "Baseline_24_2018.09.28"    
## [25] "Baseline_25_2018.09.29"     "Baseline_26_2018.09.30"    
## [27] "Baseline_27_2018.10.01"     "Baseline_28_2018.10.02"    
## [29] "Baseline_29_2018.10.03"     "Baseline_30_2018.10.04"    
## [31] "Baseline_31_2018.10.05"     "Baseline_32_2018.10.06"    
## [33] "Baseline_33_2018.10.07"     "OutsideFarm_01_2018.09.05" 
## [35] "OutsideFarm_02_2018.09.10"  "OutsideFarm_03_2018.09.11" 
## [37] "OutsideFarm_04_2018.09.12"  "OutsideFarm_05_2018.09.17" 
## [39] "OutsideFarm_06_2018.09.20"  "OutsideFarm_07_2018.09.22" 
## [41] "OutsideFarm_08_2018.09.24"  "OutsideFarm_09_2018.09.28" 
## [43] "OutsideFarm_10_2018.10.01"  "OutsideFarm_11_2018.10.03" 
## [45] "OutsideFarm_12_2018.10.06"  "OutsideFarm_13_2018.10.07" 
## [47] "TxAntibiotic_01_2018.09.06" "TxAntibiotic_02_2018.09.07"
## [49] "TxAntibiotic_03_2018.09.13" "TxAntibiotic_04_2018.09.14"
## [51] "TxAntibiotic_05_2018.09.19" "TxAntibiotic_06_2018.09.20"
## [53] "TxAntibiotic_07_2018.09.21" "TxAntibiotic_08_2018.09.26"
## [55] "TxAntibiotic_09_2018.09.29" "TxAntibiotic_10_2018.10.03"
## [57] "TxAntibiotic_11_2018.10.04" "TxAntibiotic_12_2018.10.05"

Ecological metrics - alpha diversity

## # A tibble: 3 × 2
##   type         `mean(nMicrobes)`
##   <chr>                    <dbl>
## 1 Baseline                  147.
## 2 OutsideFarm               143 
## 3 TxAntibiotic              162.

## # A tibble: 3 × 2
##   type         `mean(nMicrobes)`
##   <chr>                    <dbl>
## 1 Baseline                  1.84
## 2 Outside Farm              1.85
## 3 TxAntibiotic              1.95
## 
##  Wilcoxon rank sum exact test
## 
## data:  shannon_div_no_outliers$nMicrobes[which(shannon_div_no_outliers$type == "Baseline")] and shannon_div_no_outliers$nMicrobes[which(shannon_div_no_outliers$type == "TxAntibiotic")]
## W = 119, p-value = 0.1194
## alternative hypothesis: true location shift is not equal to 0
## 
##  Wilcoxon rank sum exact test
## 
## data:  shannon_div_no_outliers$nMicrobes[which(shannon_div_no_outliers$type == "Baseline")] and shannon_div_no_outliers$nMicrobes[which(shannon_div_no_outliers$type == "Outside Farm")]
## W = 149, p-value = 0.7654
## alternative hypothesis: true location shift is not equal to 0

Microbial Community

## [1]   192.2619 19232.5196
## [1] 63.49907 93.21980

##  [1] 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100
## [20] 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100 100
## [39] 100 100 100 100 100 100 100 100 100 100 100 100 100 100
## [1] 73.54058 97.25207
## 
##  -0.00000000000181898940354586 -0.000000000000909494701772928 
##                              1                              2 
##                              0  0.000000000000227373675443232 
##                             48                              1

## consensus_index_correct
## FALSE  TRUE 
##   540    32
## baseline_consensus_index_correct
## FALSE  TRUE 
##   537    35

Ecological metrics - beta diversity